Without knowing how the rest of the skill system is going to look I think the best way to describe what we currently know is “Meh”.
Don’t get me wrong, it’s a decent system and there is nothing wrong with it but there is nothing about it that makes me think “Woah, that perfectly reflects the megaserver-voxel-economy-MMO genre it is placed in and utilizes the opportunities that come along with it”. Atm it rather looks like any cookie-cutter skilltree in any generic f2p game.
As I wrote above. You should put more emphasis on utilizing your genre.
Besides of that it looks really unbalanced (this has already been mentioned though) a lot of the skills seem to be useless (at least in comparison to other ones of the same “tier”)
I also don’t mind the Proficiency trees rather being waterfalls. But as already adressed by someone else: They definitely need a special reward at the end. Maybe something like:
- Hammer Proficiency “Ultimate” : “Furious Miner”, Mine stone (and other ordinary rocks) with twice the speed.
- Shovel Proficiency “Ultimate”: “Archaeologist”, 1% chance to drop fossils, ancient tech components or ancient tech fragments (dependent on the difficulty of the world) when mining dirt/sand.
- Axe Proficiency “Ultimate” : “Nothing to Give”, Foliage drops Timber as well.
- Slingbow Proficiency “Ultimate” : “Ricochet”, Shots that were slightly off sometimes still hit.
- Lance Proficiency “Ultimate” : “Threading the Needle”, Perfectly timed attacks can fend off projectiles
- Brew Proficiency “Ultimate”: Dunno what brewing does so no suggestion here
- Bomb Proficiency “Ultimate”: Dunno how bombs work so no suggestion here
And so on…
Besides of that I think that there are too many “flat percentages” that make the skilltree pretty boring overall. I think you should rather go for some unique improvements instead of just flat increasing some percentages.
Reviving, for example, could look somewhat like this to be more interesting:
Basic 10% HP revive 
Reviving becomes “chargeable” to restore more health Damage reduction while charging Resurrected Players don’t draw creature-aggro for a short period of time Fully charged revives revive all players in a small radius (restored HP declines with increased distance)
I think branches like that are a lot more engaging than 10%, 30%, 50%, 75%, 100%, AoE branches.
Additionally I think that the Abilities Tree should be way less linear and branch out more.
You always put much emphasis on telling us “every player will be able to be unique”, adding ramifications (even small ones) would really benefit that goal.
“Charge weapon”, for example, would be way more engaging if it looked like this:
I don’t think this is an issue at all, in fact, I think that allowing players to do so would be a problem.
Besides of the already mentioned “Ultimates” I think that there are some things missing:
- Portal proficiency seems like something that should be a thing but isn’t.
- Warping might make a nice proficiency or skill-branch as well.
- Same for dying (death penalty)
- Creeping should definitely be a basic skill without requirements (I’d even place it in the founders tree).
- Same goes for Bulk crafting (Mass crafting, on the other hand, could still be deep down the tree)
- Connecting “Charge Weapon” and “Revive” seems a bit strange (logic- and gameplay-wise)
- Material (Natural-Gem) Proficiency shouldn’t be separate branches but rather subsequent skills in one single branch imo.
Additionally I’d love to see some skills/perks that come along with some penalties like I already wrote in an older thread of mine:
PS: I know you are a small team and that some of the things I listed may be out of your scope but I’d rather see you perfect a few gameplay-elements instead of half-assing many.